Vegetation structure derived from airborne laser scanning to assess species distribution and habitat suitability: The way forward

Ecosystem structure, especially vertical vegetation structure, is one of the six essential biodiversity variable classes and is an important aspect of habitat heterogeneity, affecting species distributions and diversity by providing shelter, foraging, and nesting sites. Point clouds from airborne laser scanning (ALS) can be used to derive such detailed information on vegetation structure. However, public agencies usually only provide digital elevation models, which do not provide information on vertical vegetation structure. Calculating vertical structure variables from ALS point clouds requires extensive data processing and remote sensing skills that most ecologists do not have. However, such information on vegetation structure is extremely valuable for many analyses of habitat use and species distribution. We here propose 10 variables that should be easily accessible to researchers and stakeholders through national data portals. In addition, we argue for a consistent selection of variables and their systematic testing, which would allow for continuous improvement of such a list to keep it up-to-date with the latest evidence. This initiative is particularly needed not only to advance ecological and biodiversity research by providing valuable open datasets but also to guide potential users in the face of increasing availability of global vegetation structure products

genotype_file_MER_Geraldesetal2012.csv

The file genotype_file_MER_Geraldesetal2012.csv contains the genotyping data used in Geraldes et al. 2012 "A 34K SNP genotyping array for Populus trichocarpa: Design, application to the study of natural populations and transferability to other Populus species". The file contains genotypes for 32,683 loci in 72 accessions. These loci were genotyped with the 34K Populus SNP array described in this manuscript. Details regarding each locus and the genotyping methods can be found in the manuscript. The file contains 32,684 lines and 73 fields per line separated with commas (.csv). The first line is a header line. The first field reads "SNP" and indicates that for each line, the first field contains the name of the Single Nucleotide Polymorphism (SNP). This name has three parts separated with underscores, where the first part is always "scaffold", the second part is the linkage group to which the locus is mapped and the last part is the location (in base pairs) in that linkage group. All names refer to version 2 of the Populus trichocarpa genome available at http://www.phytozome.net/. Each following field in line one, is the name of the accession genotyped. Accession details are provided in Geraldes et al 2012. Each subsequent line has the genotypes for each individual/locus. Each genotype is followed by a "|" and a number ranging from 0 to 1. This number is the GenCall Score, a measure of the confidence in the genotytpe call. Details are in Geraldes et al. 2012. If the Gencall Score is <0.15, the genotype is considered missing and is represented by "--". Other missing genotypes are indicated with #NA

Paternity recovery in two maritime pine polycross mating designs and consequences for breeding

Polycross mating systems are widely used in forest tree breeding for genetic testing. Backward selection based on polycross testing assumes equal male reproductive success and true half-sib progeny. The main objectives of this study were, firstly, to investigate the departure from these assumptions in a maritime pine polycross trial and, secondly, to evaluate the consequences for heritability and breeding values estimations. A total of 984 offspring from 98 half-sib families was genotyped with single nucleotide polymorphism markers to recover the full pedigree. Paternity was assigned successfully for 89 % of the offspring at a 99 % confidence level. We thus concluded there was an 11 % pollen contamination rate, assuming contamination when no genotype from the polymix composition could be identified as a father. The paternal contribution to the offspring varied among the males, but the departure from half-sib assumption was moderate since the average genetic correlation within the family was 0.26. Heritability and breeding values for girth at breast height and stem sweep were estimated using individual-tree mixed models with either partial or full pedigree information. The results highlighted a minor bias in heritability estimation due to unknown paternity, as well as a high correlation for estimated breeding values between the partial and full pedigree models, suggesting that the genetic merit of the parental generation for backward selection was adequately predicted using the partial pedigree model. Finally, pedigree recovery was also discussed in a perspective of forward selection